Contractors now say the giant tunnel drill known as Bertha won’t get moving again until next spring, another setback in the state’s Highway 99 project beneath downtown Seattle.

The machine’s main drive bearing needs to be replaced, and Seattle Tunnel Partners (STP) earlier said it expected to have Bertha on the move by September. That goal was delayed Monday, until the end of March.

The repair plan will still employ a deep pit, lined with vertical concrete pillars, where the front end will be dismantled.

But there’s been a change in strategy. Contractors now intend to peel away the steel skin, or shield, from the cylindrical tunnel drill. They’ll hoist the entire cutter head, drive axle and bearing in one piece — some 2,000 tons altogether — and set those on the surface.

Then the bearing will be replaced at street level, before the assembly is lowered and reattached early next year. Chris Dixon, STP’s project director, said this method will allow a more accurate fit, compared with fastening multiple parts 120 feet underground.

It’s still unclear what these delays — about 16 months, based on the current estimate — might cost the public, whose gasoline taxes fund the work.

Dixon said STP is still trying to understand why the machine stopped, and that the extent of the damage won’t be known until the front end is disassembled.

The state Department of Transportation (DOT) continues to maintain that STP is responsible for the expense of repair and delay, said Todd Trepanier, Highway 99 program administrator. The contract is currently worth $1.44 billion.

Dixon replied that the costs will be negotiated, based on language in the sophisticated contract. There is every reason to believe, based on past statements by both sides, that any remaining disputes will be decided by either an expert review board or in a courtroom.

Trepanier acknowledged that the project isn’t moving along as quickly as the public or DOT hoped. “What we are envisioning is to get this tunnel complete,” he said.

Dixon said the four-lane tunnel could still open to traffic by November 2016, since crews continue to build the portals at Sodo and South Lake Union as Bertha pauses. November 2016 was the state’s completion deadline under tunnel supporter Gov. Chris Gregoire at the time bids were filed in 2010. STP won the job partly because it promised to finish faster, by the end of 2015.

Workers this week are injecting grout into gaps between buried pillars that STP previously installed. One row forms a protective wall alongside the viaduct, and another fronting Elliott Bay. The grout should make the walls watertight. If that’s successful, groundwater won’t drain out of Pioneer Square and cause historic buildings or the viaduct to settle, nor would it swamp Bertha in the repair pit.

Some buildings temporarily sank as much as a quarter-inch just before Christmas when groundwater was pumped away to prepare for underground inspections of Bertha.

This time the only groundwater to be pumped away will be from within the watertight repair pit itself, Dixon said.

One big challenge will be simply to get Bertha into the open-air repair site, said Dixon. The machine will be driven about 45 feet forward, grinding through some of the concrete pillars. The main bearing is contaminated by grit, and the front end overheated while moving just a few feet in early December and late January.

Bertha remains under warranty by Hitachi Zosen, which manufactured the $80 million tunnel-boring machine in Osaka, Japan. At 57 feet, 4 inches in diameter, it’s the biggest in the world.

Going forward, a crucial question is whether this huge cylindrical device — simply a larger version what’s evolved over the last half-century of tunnel-boring machines — can support the tremendous weight of its own 630-ton cutter face and supporting parts as they exert torque and vibration. During assembly in Japan, some drive parts went out of alignment, and surrounding parts were reinforced.

Dixon said Monday that engineers haven’t determined yet whether or how the frame itself must be further strengthened.

Before the job started, Boston megaproject expert Thom Neff issued a report emphasizing the Seattle tunnel is “beyond precedent” and therefore posed both known and unforeseeable financial risks. His report was requested by then-Mayor Mike McGinn, who criticized the tunnel, calling for a societal shift away from auto dependence.

Although the DOT’s contract employs many safeguards, the soils of Seattle contain groundwater, small boulders and abrasive sediments worse than seen in Boston’s Big Dig, the Neff report said.

Current Mayor Ed Murray supported the tunnel while he served in the Legislature. The 2009 tunnel law followed years of public disputes over other options, including a new elevated highway, a major retrofit, a shallow tunnel or a surface boulevard.

“I still think it’s the right decision,” Murray said Monday, because the deep-bore tunnel keeps traffic moving during construction and creates space for parks to be built afterward.

Murray said he’s believed for some time the Sept. 1 goal to get Bertha moving again wouldn’t hold up.

“This is a very bad thing that happened, but it’s not unusual for bad things to happen in megaprojects,” Murray said.

At a meeting earlier this year, Murray said he told the state and contractors: “I needed folks to look at solutions and stop talking about litigation. Litigation doesn’t build the tunnel.”

Longtime opponent Elizabeth Campbell, of Magnolia, filed a federal lawsuit last month, alleging that state DOT shouldn’t be allowed to dig a repair pit without undergoing environmental review.

“We’re putting together an injunction, but they’ve injuncted their own project,” she joked Monday.

The state Transportation Commission is recommending that an outside expert-review panel stay on the job until tunneling resumes, said Commissioner Charles Royer, a former Seattle mayor who lives in Pioneer Square.

Royer said delays in the tunnel could delay hold back efforts to organize a local-improvement property tax to beautify the waterfront, as landowners will first want to see construction winding down. But he also expressed confidence in STP, mentioning that a new laser-guided sensing device was just installed on his apartment building to warn of any shifts.

“I’ve waited a long time for this,” Royer said. “I can wait a little bit longer.”